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      BEETL-fastq: a searchable compressed archive for DNA reads.

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          Abstract

          FASTQ is a standard file format for DNA sequencing data, which stores both nucleotides and quality scores. A typical sequencing study can easily generate hundreds of gigabytes of FASTQ files, while public archives such as ENA and NCBI and large international collaborations such as the Cancer Genome Atlas can accumulate many terabytes of data in this format. Compression tools such as gzip are often used to reduce the storage burden but have the disadvantage that the data must be decompressed before they can be used. Here, we present BEETL-fastq, a tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. Importantly, the full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input.

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          Author and article information

          Journal
          Bioinformatics
          Bioinformatics (Oxford, England)
          1367-4811
          1367-4803
          Oct 2014
          : 30
          : 19
          Affiliations
          [1 ] Computational Biology Group, Illumina Cambridge Ltd., Little Chesterford, Essex CB10 1XL, UK.
          Article
          btu387
          10.1093/bioinformatics/btu387
          24950811
          1a7ae737-31b9-4d45-a38b-73998c447fcb
          © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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